Faculty Research Publications (Crop and Soil Science)http://hdl.handle.net/1957/18801
Tue, 31 Mar 2015 21:09:28 GMT2015-03-31T21:09:28ZEmergence of Groundnut ringspot virus and Tomato chlorotic spot virus in Vegetables in Florida and the Southeastern United Stateshttp://hdl.handle.net/1957/55460
Emergence of Groundnut ringspot virus and Tomato chlorotic spot virus in Vegetables in Florida and the Southeastern United States
Webster, Craig G.; Frantz, Galen; Reitz, Stuart R.; et al.
Groundnut ringspot virus (GRSV) and Tomato chlorotic spot virus
(TCSV) are two emerging tospoviruses in Florida. In a survey of the
southeastern United States, GRSV and TCSV were frequently detected in
solanaceous crops and weeds with tospovirus-like symptoms in south
Florida, and occurred sympatrically with Tomato spotted wilt virus (TSWV)
in tomato and pepper in south Florida. TSWV was the only tospovirus
detected in other survey locations, with the exceptions of GRSV from tomato
(Solanum lycopersicum) in South Carolina and New York, both of
which are first reports. Impatiens (Impatiens walleriana) and lettuce
(Lactuca sativa) were the only non-solanaceous GRSV and/or TCSV
hosts identified in experimental host range studies. Little genetic diversity
was observed in GRSV and TCSV sequences, likely due to the recent
introductions of both viruses. All GRSV isolates characterized were reassortants
with the TCSV M RNA. In laboratory transmission studies,
Frankliniella schultzei was a more efficient vector of GRSV than F. occidentalis.
TCSV was acquired more efficiently than GRSV by F. occidentalis
but upon acquisition, transmission frequencies were similar. Further
spread of GRSV and TCSV in the United States is possible and detection
of mixed infections highlights the opportunity for additional reassortment
of tospovirus genomic RNAs.
To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article was published by the American Phytopathological Society and is in the public domain. The published article can be found at: http://apsjournals.apsnet.org/loi/phyto.
Sun, 01 Mar 2015 00:00:00 GMThttp://hdl.handle.net/1957/554602015-03-01T00:00:00ZFOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focushttp://hdl.handle.net/1957/55278
FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus
Prestat, Emmanuel; David, Maude M.; Hultman, Jenni; Myrold, David D.; et al.
A new functional gene database, FOAM (Functional
Ontology Assignments for Metagenomes), was developed
to screen environmental metagenomic sequence
datasets. FOAM provides a new functional
ontology dedicated to classify gene functions relevant
to environmental microorganisms based on Hidden
Markov Models (HMMs). Sets of aligned protein
sequences (i.e. ‘profiles’) were tailored to a large
group of target KEGG Orthologs (KOs) from which
HMMs were trained. The alignments were checked
and curated to make them specific to the targeted
KO. Within this process, sequence profiles were enriched
with the most abundant sequences available
to maximize the yield of accurate classifier models.
An associated functional ontology was built to describe
the functional groups and hierarchy. FOAM
allows the user to select the target search space
before HMM-based comparison steps and to easily
organize the results into different functional categories
and subcategories. FOAM is publicly available
at http://portal.nersc.gov/project/m1317/FOAM/.
To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Oxford University Press. The published article can be found at: http://nar.oxfordjournals.org/.
Wed, 29 Oct 2014 00:00:00 GMThttp://hdl.handle.net/1957/552782014-10-29T00:00:00ZDirect links between the vernalization response and other key traits of cereal cropshttp://hdl.handle.net/1957/55260
Direct links between the vernalization response and other key traits of cereal crops
Deng, Weiwei; Casao, M. Cristina; Wang, Penghao; Sato, Kazuhiro; Hayes, Patrick M.; Finnegan, E. Jean; Trevaskis, Ben
Transcription of the VERNALIZATION1 gene (VRN1) is induced by prolonged cold
(vernalization) to trigger flowering of cereal crops, such as wheat and barley. VRN1 encodes a
MADS box transcription factor that promotes flowering by regulating the expression of other
genes. Here we use transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation
sequencing (ChIP-seq) to identify direct targets of VRN1. Over 500 genomic regions
were identified as potential VRN1-binding targets by ChIP-seq. VRN1 binds the promoter of
FLOWERING LOCUS T-like 1, a promoter of flowering in vernalized plants. VRN1 also targets
VERNALIZATION2 and ODDSOC2, repressors of flowering that are downregulated in
vernalized plants. RNA-seq identified additional VRN1 targets that might play roles
in triggering flowering. Other targets of VRN1 include genes that play central roles in
low-temperature-induced freezing tolerance, spike architecture and hormone metabolism.
This provides evidence for direct regulatory links between the vernalization response pathway
and other important traits in cereal crops.
This is the publisher’s final pdf. The published article is copyrighted by Macmillan Publishers Limited and can be found at: http://www.nature.com/ncomms/index.html.
Tue, 06 Jan 2015 00:00:00 GMThttp://hdl.handle.net/1957/552602015-01-06T00:00:00ZA Numerical Examination of ¹⁴CO₂ Chamber Methodologies for Sampling at the Soil Surfacehttp://hdl.handle.net/1957/55236
A Numerical Examination of ¹⁴CO₂ Chamber Methodologies for Sampling at the Soil Surface
Egan, Jocelyn; Nickerson, Nick; Phillips, Claire; Risk, Dave
Radiocarbon is an exceptionally useful tool for studying soil-respired CO₂, providing information about soil
carbon turnover rates, depths of production, and the biological sources of production through partitioning. Unfortunately, little
work has been done to thoroughly investigate the possibility of inherent biases present in current measurement techniques,
like those present in δ¹³CO₂ methodologies, caused by disturbances to the soil’s natural diffusive regime. This study investigates
the degree of bias present in four ¹⁴C sampling chamber methods using a three-dimensional numerical soil-atmosphere
CO₂ diffusion model. The four chambers were tested in an idealized, surrogate reality by assessing measurement bias with
varying Δ¹⁴C and δ¹³C signatures of production, collar lengths, soil biological productivity rates, and soil diffusivities. The
static and Iso-FD chambers showed almost no isotopic measurement bias, significantly outperforming dynamic chambers,
which demonstrated biases up to 200‰ in some modeled scenarios. The study also showed that ¹³C and ¹⁴C diffusive fractionation
are not a constant multiple of one another, but that the δ¹³C correction still works in diffusive scenarios because the
change in fractionation is not large enough to impact measured Δ¹⁴C values during chamber equilibration.
This is the publisher’s final pdf. The published article is copyrighted by the Arizona Board of Regents on behalf of the University of Arizona and can be found at: https://journals.uair.arizona.edu/index.php/radiocarbon/index.
Wed, 01 Jan 2014 00:00:00 GMThttp://hdl.handle.net/1957/552362014-01-01T00:00:00Z